Hmmm--not the obvious error!
One idea is that you might accidentally have put some loads with another load case.
Another idea: Are some loads member loads and some joint loads? If so, then if you need to make sure the "Show Joint Loads With Span Loads" checkbox is checked under Display, Show Frame Loads.
Surely your model isn't rotated so that some loads simply aren't visible.
I hope one of those is it because I have no other idea!